Vaccinia virus is used to vaccinate persons to prevent disease with smallpox. Compared with other live virus vaccines, the smallpox vaccine is associated with frequent side effects including fever, a sore or swollen arm, headache, and fatigue. Other more serious side effects have also been reported including development of multiple lesions outside the vaccination site (generalized vaccinia), inflammation of the brain (postvaccinia encephalitis), severe infection of the skin in persons with a history of eczema (eczema vaccinatum), and disseminated vaccinia virus infection in immunocompromised persons (progressive vaccinia). Relatively few studies of vaccine-induced immune responses have been done in the modern era using contemporary techniques. Cytokines are proteins that are produced by white blood cells and secreted into the bloodstream that are important for trafficking of white blood cells in response to inflammation. We hypothesize that induction of cytokines is associated with some of the side effects of smallpox vaccination. Identification of specific cytokines induced after vaccination may help to explain the pathogenesis of certain side effects associated with smallpox vaccination and might suggest new ways to modify some of these side effects. The diagnosis of complications related to smallpox vaccination may be difficult because the rash may resemble other infectious or noninfectious diseases. We have obtained vaccinia virus specimens from the arm at the site of inoculation with the virus and attempted to detect the virus using three different assays. We compared shell vial cultures (in which the specimen is centrifuged onto a coverslip containing cells that can be infected with vaccinia), real-time PCR (using primers that detect all members of the virus family that includes vaccinia), and direct fluorescent antibody (using fluorescence-labeled antibody to vaccinia). Of 47 samples assayed, 100% were positive by PCR, 89% were positive by shell vial, and 40% were positive by direct fluorescent antibody). Direct fluorescent antibody was limited by the need for adequate numbers of cells, with 32% of the samples inadequate for interpretation. Real-time PCR was sensitive to a level of 25 virus copies per ml. We did not detect any false positive results with PCR. PCR was positive for longer times post-vaccination than the shell vial assay. The shell vial assay was estimated to have a sensitivity of about 82%. Sonication of specimens before inoculation onto shell virals increased the sensitivity of the shell vial assay. Infectious virus could be recovered after 45 minutes of acetone fixation of shell vial cell monolayers. Fluorescence-labeled vaccinia polyclonal antibodies from three different vendors were used in the shell vial assay. These antibodies detected vaccinia, cowpox, camelpox, and monkeypox viruses; however, all antibodies cross-reacted with herpes simplex virus type-1. Commercially available monoclonal antibodies to vaccinia were specific for vaccinia virus. PCR was the most sensitive test for detecting vaccinia in clinical specimens, while direct fluorescent antibody testing was more rapid, but the least sensitive test.